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Africans’ genes mute on human birthplace

DNA studies fail to locate root of the species

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2:10pm, September 20, 2012
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The origin story for Homo sapiens is a messy tale. Rather than emerging from one small population, the human species likely evolved from a dispersed, complex network of groups that mixed and mated with each other, scientists report online September 20 in Science.

The new research is one of the largest genetic studies of southern Africa’s click-speaking hunter-gatherers known as the Khoisan. Sometimes called Bushmen, the Khoisan are the world’s most genetically diverse people and diverged from other populations very early in human history.

The new work dates the genetic split between the Khoisan and the rest of humankind to at least 100,000 years ago, which is in line with other estimates. That’s 55,000 years older than the next branch on the human family tree, when Central African pygmies split off. The researchers also found that the Khoisan divided into a northern and a southern group approximately 35,000 years ago.  

But when the scientists looked for genetic clues pointing to where in sub-Saharan Africa humankind began, they couldn’t trace modern groups back to any one region. That suggests early humans came from a highly structured population with genetic exchange between subgroups.

“The complexity of the South African population is the big story,” says Adam Siepel, a computational biologist at Cornell University. “It undermines simpler stories trying to pinpoint a single geographic origin of modern humans.” Previous fossil evidence had suggested East Africa while smaller genetic analyses indicated South Africa.

In the new study, Carina Schlebusch of Sweden’s Uppsala University and colleagues looked at single nucleotide polymorphisms, or SNPs, which are locations in the genetic code where people commonly differ. The researchers surveyed 2.3 million SNPs in 220 individuals from 11 African populations, including seven Khoisan groups. After combining the new data with previously published data, the team assessed four measures of genetic variation to find where in Africa humans originated, but the results didn’t converge on one location.

A paper set to appear in an upcoming issue of Nature Communications reaches similar conclusions. Joseph Pickrell of Harvard Medical School and colleagues analyzed a different set of more than 565,000 SNPs in 187 individuals from 22 African populations. Like Schlebusch’s team, Pickrell’s group identified a split within the Khoisan that occurred roughly 30,000 years ago, breaking the population into a northwestern and a southeastern group. Their work also failed to find a single area where humans arose.

But you wouldn’t necessarily expect to find the cradle of humanity by looking at the evolutionary relationships of present-day Africans, says Sarah Tishkoff, a human geneticist at the University of Pennsylvania in Philadelphia. “When you look at modern populations, you see where they live today,” she says. “You don’t know where they were 50,000 or 60,000 years ago.”

Schlebusch’s team also searched for genetic changes that might reveal the evolutionary forces that shaped early Africans. The researchers found hints that selection acting on a few genes related to skeletal and neurological development may have played a role in the emergence of anatomically modern humans. That makes sense, says anthropologist John Hawks of the University of Wisconsin–Madison: “They confirm selection on a gene that differs between modern humans and the Neandertals, RUNX2, which may be involved in the unique physical form of our species relative to archaic humans.”

More extensive analyses that examine the complete genetic instruction book of people from different Khoisan groups are needed to confirm such findings, Tishkoff says. So far, scientists have only done this for one Khoisan man.

“We’re just at the beginning of understanding modern human history and origins in Africa,” Tishkoff says. “In the future, as we do more whole genome sequencing, it will become clearer.”

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